I concur with Rusty: they could be the same, but in some contexts we favor one over the other.

"for your eyes only" suggests that other people shouldn't be allowed to see it, while "only for your eyes" suggests that something is useful only in relation someone's eyes rather than to some other part of the body.

Concurring with everyone else, while I've heard for your eyes only a thousand times (thank Ian Fleming for that), I'd never heard only for your eyes. In fact, if you hadn't provided the context, I would have guessed that was a line from a romantic tune.